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. 2024 Jan;18(1):e13252.
doi: 10.1111/irv.13252.

Genome characterization of influenza A and B viruses in New South Wales, Australia, in 2019: A retrospective study using high-throughput whole genome sequencing

Xinye Wang  1   2 , Ki Wook Kim  2   3 , Gregory Walker  1   2 , Sacha Stelzer-Braid  1   2 , Matthew Scotch  4   5   6 , William D Rawlinson  1   2
Affiliations

Genome characterization of influenza A and B viruses in New South Wales, Australia, in 2019: A retrospective study using high-throughput whole genome sequencing

Xinye Wang et al. Influenza Other Respir Viruses. 2024 Jan.

Abstract

Background: During the 2019 severe influenza season, New South Wales (NSW) experienced the highest number of cases in Australia. This study retrospectively investigated the genetic characteristics of influenza viruses circulating in NSW in 2019 and identified genetic markers related to antiviral resistance and potential virulence.

Methods: The complete genomes of influenza A and B viruses were amplified using reverse transcription-polymerase chain reaction (PCR) and sequenced with an Illumina MiSeq platform.

Results: When comparing the sequencing data with the vaccine strains and reference sequences, the phylogenetic analysis revealed that most NSW A/H3N2 viruses (n = 68; 94%) belonged to 3C.2a1b and a minority (n = 4; 6%) belonged to 3C.3a. These viruses all diverged from the vaccine strain A/Switzerland/8060/2017. All A/H1N1pdm09 viruses (n = 20) showed genetic dissimilarity from vaccine strain A/Michigan/45/2015, with subclades 6B.1A.5 and 6B.1A.2 identified. All B/Victoria-lineage viruses (n = 21) aligned with clade V1A.3, presenting triple amino acid deletions at positions 162-164 in the hemagglutinin protein, significantly diverging from the vaccine strain B/Colorado/06/2017. Multiple amino acid substitutions were also found in the internal proteins of influenza viruses, some of which have been previously reported in hospitalized influenza patients in Thailand. Notably, the oseltamivir-resistant marker H275Y was present in one immunocompromised patient infected with A/H1N1pdm09 and the resistance-related mutation I222V was detected in another A/H3N2-infected patient.

Conclusions: Considering antigenic drift and the constant evolution of circulating A and B strains, we believe continuous monitoring of influenza viruses in NSW via the high-throughput sequencing approach provides timely and pivotal information for both public health surveillance and clinical treatment.

Keywords: New South Wales; drug resistance, viral; high-throughput nucleotide sequencing; influenza, human.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

FIGURE 1
FIGURE 1
Phylogenetic analysis of the hemagglutinin (HA) gene from influenza A (H1N1pdm09) viruses detected in this study. The phylogenetic tree was constructed by the maximum likelihood method using IQ‐TREE with substitution model selection (ModelFinder implemented in IQ‐TREE) option and 1000 bootstraps. The best‐fit model according to Bayesian information criterion: HKY + F + G4 (HA). Bootstrap values are shown if >70%.
FIGURE 2
FIGURE 2
Phylogenetic analysis of the neuraminidase (NA) gene from influenza A (H1N1pdm09) viruses detected in this study. The phylogenetic tree was constructed by the maximum likelihood method using IQ‐TREE with substitution model selection (ModelFinder implemented in IQ‐TREE) option and 1000 bootstraps. The best‐fit model according to Bayesian information criterion: HKY + F + G4 (NA). Bootstrap values are shown if >70%.
FIGURE 3
FIGURE 3
Phylogenetic analysis of the hemagglutinin (HA) gene from influenza A (H3N2) viruses detected in this study. The phylogenetic tree was constructed by the maximum likelihood method using IQ‐TREE with substitution model selection (ModelFinder implemented in IQ‐TREE) option and 1000 bootstraps. The best‐fit model according to Bayesian information criterion: TVM + F + G4 (HA). Bootstrap values are shown if >70%.
FIGURE 4
FIGURE 4
Phylogenetic analysis of the neuraminidase (NA) gene from influenza A (H3N2) viruses detected in this study. The phylogenetic tree was constructed by the maximum likelihood method using IQ‐TREE with substitution model selection (ModelFinder implemented in IQ‐TREE) option and 1000 bootstraps. The best‐fit model according to Bayesian information criterion: TVM + F + G4 (NA). Bootstrap values are shown if >70%.
FIGURE 5
FIGURE 5
Phylogenetic analysis of the hemagglutinin (HA) gene from influenza B (Victoria lineage) viruses detected in this study. The phylogenetic tree was constructed by the maximum likelihood method using IQ‐TREE with substitution model selection (ModelFinder implemented in IQ‐TREE) option and 1000 bootstraps. The best‐fit model according to Bayesian information criterion: K3Pu + F + G4 (HA). Bootstrap values are shown if >70%.
FIGURE 6
FIGURE 6
Phylogenetic analysis of the neuraminidase (NA) gene from influenza B (Victoria lineage) viruses detected in this study. The phylogenetic tree was constructed by the maximum likelihood method using IQ‐TREE with substitution model selection (ModelFinder implemented in IQ‐TREE) option and 1000 bootstraps. The best‐fit model according to Bayesian information criterion: HKY + F (NA). Bootstrap values are shown if >70%.
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